ArrayXPath II: Mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using Scalable Vector Graphics

Nucleic Acids Research

Volumn 33, Issue SUPPL. 2, 2005, Pages

  Chung, Hee Joon ^a   Park, Chan Hee ^a   Han, Mi Ryung ^a   Lee, Seokho ^a   Ohn, Jung Hun ^a   Kim, Jihoon ^a   Kim, Jihun ^a   Kim, Ju Han ^a  

^a Seoul National University College of Medicine   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER GRAPHICS; COMPUTER PROGRAM; CONTROLLED STUDY; FISHER EXACT TEST; GENE EXPRESSION PROFILING; GENE INTERACTION; GENE MAPPING; GENETIC CORRELATION; INFORMATION PROCESSING; INTERNET; MEDICAL TECHNOLOGY; MICROARRAY ANALYSIS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; STATISTICAL SIGNIFICANCE; CORRELATION ANALYSIS; GENETIC DISORDER; HUMAN; NONHUMAN; CLUSTER ANALYSIS; COMPUTER INTERFACE; DNA MICROARRAY; GENETIC DATABASE; GENETIC PREDISPOSITION; MESH HEADING; METHODOLOGY; SYSTEM ANALYSIS;

CLUSTER ANALYSIS; COMPUTER GRAPHICS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENETIC PREDISPOSITION TO DISEASE; INTERNET; MEDICAL SUBJECT HEADINGS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE; SYSTEMS INTEGRATION; USER-COMPUTER INTERFACE;

EID: 23144444420     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki450     Document Type: Article

References (13)

1. Roy,P.J., Stuart,J.M., Lurd,J. and Kim,S.K. (2002) Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature, 418, 975-979.
2. Lercher,M.J., Urrutia,A. and Hurst,L.D. (2002) Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nature Genet., 31, 180-183.
3. Tavazoie,S., Hughes,J.D., Campbell,M.J., Cho,R.J. and Church,G.M. (1999) Systematic determination of genetic network architecture. Nature Genet., 22, 281-285.
4. Segal,E., Shapira,M., Regev,A., Pe'er,D., Botstein,D., Koller,D. and Friedman,N. (2003) Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data. Nature Genet., 34, 166-176.
5. Mewes,H.W., Frishman,D., Guldener,U., Mannhaupt,G., Mayer,K., Mokrejs,M., Morgenstern,B., Munsterkotter,M., Rudd,S. and Weil,B. (2002) MIPS: A database for genomes and protein sequences. Nucleic Acids Res., 30, 31-34.
6. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. (2000) Gene Ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nature Genet., 25, 25-29.
7. Chung,H.J., Kim,M., Park,C.H., Kim,J. and Kim,J.H. (2004) ArrayXPath: mapping and visualizing microarray gene expression data with integrated biological pathway resources using Scalable Vector Graphics. Nucleic Acids Res., 32, W464-W464.
8. Dennis,G.,Jr, Sherman,B.T., Hosack,D.A., Yang,J., Gao,W., Lane,H.C. and Lempicki,R.A. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol., 4, R60.
9. Zeeberg,B.R., Feng,W., Wang,G., Wang,M.D., Fojo,A.T., Sunshine,M., Narasimhan,S., Kane,D.W., Reinhold,W.C., Lababidi,S. et al. (2003) GoMiner: A resource for biological interpretation of genomic and proteomic data. Genome Biol., 4, R28.
10. Hewett,M., Oliver,D.E., Rubin,D.L., Easton,K.L., Stuart,J.M., Altman,R.B. and Klein,T.E. (2002) PharmGKB: The Pharmacogenetics Knowledge Base. Nucleic Acids Res., 32, 163-165.
11. Storey,J.D. and Tibshirani,R. (2003) Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA, 100, 9440-9445.
12. Zheng,C.J., Zhou,H., Xie,B., Han,L.Y., Yap,C.W. and Chen,Y.Z. (2004) TRMP: A database of therapeutically relevant multiple pathway. Bioinformatics, 20, 2236-2241.
13. Robinson,P.N., Wollstein,A., Bohme,U. and Beattie,B. (2004) Ontologizing gene-expression microarray data: Characterizing clusters with Gene Ontology. Bioinformatics, 20, 979-981.